rs532625

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001845.6(COL4A1):c.432T>A(p.Ala144Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,613,492 control chromosomes in the GnomAD database, including 180,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 14787 hom., cov: 31)

Exomes 𝑓: 0.47 ( 165689 hom. )

Consequence

COL4A1
NM_001845.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: -0.0960

Variant links:

Genes affected

COL4A1 (HGNC:2202): (collagen type IV alpha 1 chain) This gene encodes a type IV collagen alpha protein. Type IV collagen proteins are integral components of basement membranes. This gene shares a bidirectional promoter with a paralogous gene on the opposite strand. The protein consists of an amino-terminal 7S domain, a triple-helix forming collagenous domain, and a carboxy-terminal non-collagenous domain. It functions as part of a heterotrimer and interacts with other extracellular matrix components such as perlecans, proteoglycans, and laminins. In addition, proteolytic cleavage of the non-collagenous carboxy-terminal domain results in a biologically active fragment known as arresten, which has anti-angiogenic and tumor suppressor properties. Mutations in this gene cause porencephaly, cerebrovascular disease, and renal and muscular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

COL4A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 13-110211878-A-T is Benign according to our data. Variant chr13-110211878-A-T is described in ClinVar as [Benign]. Clinvar id is 258254.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-110211878-A-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.096 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL4A1	NM_001845.6 link	c.432T>A	p.Ala144Ala	synonymous_variant	Exon 7 of 52	ENST00000375820.10	NP_001836.3
COL4A1	NM_001303110.2 link	c.432T>A	p.Ala144Ala	synonymous_variant	Exon 7 of 25		NP_001290039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL4A1	ENST00000375820.10 link	c.432T>A	p.Ala144Ala	synonymous_variant	Exon 7 of 52	1	NM_001845.6	ENSP00000364979.4		P02462-1

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66384

AN:

151860

Hom.:

14785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.371

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.464

Gnomad OTH

AF:

0.475

GnomAD3 exomes

AF:

0.467

AC:

117374

AN:

251402

Hom.:

28211

AF XY:

0.476

AC XY:

64756

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.404

Gnomad ASJ exome

AF:

0.528

Gnomad EAS exome

AF:

0.496

Gnomad SAS exome

AF:

0.591

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.466

Gnomad OTH exome

AF:

0.480

GnomAD4 exome

AF:

0.474

AC:

692386

AN:

1461514

Hom.:

165689

Cov.:

AF XY:

0.478

AC XY:

347442

AN XY:

727068

show subpopulations

Gnomad4 AFR exome

AF:

0.359

Gnomad4 AMR exome

AF:

0.401

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.544

Gnomad4 SAS exome

AF:

0.584

Gnomad4 FIN exome

AF:

0.417

Gnomad4 NFE exome

AF:

0.470

Gnomad4 OTH exome

AF:

0.481

GnomAD4 genome

AF:

0.437

AC:

66399

AN:

151978

Hom.:

14787

Cov.:

AF XY:

0.437

AC XY:

32450

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.371

Gnomad4 AMR

AF:

0.416

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.516

Gnomad4 SAS

AF:

0.595

Gnomad4 FIN

AF:

0.409

Gnomad4 NFE

AF:

0.464

Gnomad4 OTH

AF:

0.472

Alfa

AF:

0.463

Hom.:

5463

Bravo

AF:

0.433

Asia WGS

AF:

0.542

AC:

1884

AN:

3478

EpiCase

AF:

0.481

EpiControl

AF:

0.482

ClinVar

Significance: Benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 19, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 02, 2021

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Brain small vessel disease 1 with or without ocular anomalies

Benign:2

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome

Benign:2

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not provided

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Porencephalic cyst

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.34

DANN

Benign

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over